[@abdallah]

Hi,

Hi,

I am having a similar problem. It seems that the sam file and the database are fine but then I get this error

java NGSrich -r /Data/Exp1/s_3_QC_remdup.sam -a hg19 -T /Data/Exp1/ -t /Data/Exp1/exomeplusv2.bed
test: /Data/Exp1/enrichment
=======================1=======================
>>> STEP 1: reducing files

READS FILE:
/Data/Exp1/s_3_QC_remdup.sam was reduced to /Data/Exp1/1306423511007/NGSrich_s_3_QC_remdup_KDavid.26819.txt
Reduced file /Data/Exp1/1306423511007/NGSrich_s_3_QC_remdup_KDavid.26819.txt sorted

GENOME ANNOTATION FILE:
/Data/Exp1/1306423511007/refGene.genome reduced to /Data/Exp1/1306423511007/NGSrich_genome_KDavid.26819.txt
Exception in thread "main" java.lang.ArrayIndexOutOfBoundsException: Array index out of range: 1
at java.util.Vector.get(Vector.java:721)
at adapter.Adapter.field(Adapter.java:90)
at adapter.TargetAdapter.start(TargetAdapter.java:168)
at adapter.TargetAdapter.adapt(TargetAdapter.java:56)
at Enrichment.reduceFiles(Enrichment.java:185)
at NGSrich.main(NGSrich.java:91)

This is a head result of my .bed file

head /Data/Exp1/exomeplusv2.bed
track:exome
chr1 30275 30431
chr1 69069 70029
chr1 228233 228354
chr1 228471 228711
chr1 367647 368608
chr1 470971 471330
chr1 621084 622045
chr1 741165 741285
chr1 745438 745558

Any ideas?

Thanks,

Dave

You should just remove the first line of the target file because it doesn't have the expected form (ie "chrome start end"). In the next version we will probably allow comments within the files.

Regards,
@abdallah

[PeteH]

Hi Peter,

This looks like a very useful tool! Do you have plans to allow the input file to be in BAM rather than SAM format? Also, is it possible to include the median coverage along with the mean coverage?

Thanks,
Pete

[jtjli]

i keep getting this error after ~20mins. Any idea?

Thanks,
Jason


java NGSrich -r 32815T_GATKrealigned_duplicates_marked.sam -g hg19 -t 0247401_D_BED_20090724_hg19.bed -T ngsrich_tmp -o ngsrich_out


=======================1=======================
>>> STEP 1: reducing files

READS FILE:
/mnt/Storage/All_Users/lij/testNGSrich/32815T_GATKrealigned_duplicates_marked.sam was reduced to /mnt/Storage/All_Users/lij/testNGSrich/ngsrich_tmp/1306393150286/NGSrich_32815T_GATKrealigned_duplicates_marked_pmc-bioinf02.14020.txt
Reduced file /mnt/Storage/All_Users/lij/testNGSrich/ngsrich_tmp/1306393150286/NGSrich_32815T_GATKrealigned_duplicates_marked_pmc-bioinf02.14020.txt sorted


java.io.FileNotFoundException: /mnt/Storage/All_Users/lij/testNGSrich/ngsrich_tmp/1306393150286/refGene.genome (No such file or directory)
at java.io.FileInputStream.open(Native Method)
at java.io.FileInputStream.<init>(FileInputStream.java:106)
at java.util.Scanner.<init>(Scanner.java:636)
at adapter.GenomeAdapter.adapt(GenomeAdapter.java:22)
at Enrichment.reduceFiles(Enrichment.java:181)
at NGSrich.main(NGSrich.java:91)
Exception in thread "main" java.lang.NullPointerException
at adapter.GenomeAdapter.adapt(GenomeAdapter.java:33)
at Enrichment.reduceFiles(Enrichment.java:181)
at NGSrich.main(NGSrich.java:91)

[dnusol]

Hi,

I am having a similar problem. It seems that the sam file and the database are fine but then I get this error

java NGSrich -r /Data/Exp1/s_3_QC_remdup.sam -a hg19 -T /Data/Exp1/ -t /Data/Exp1/exomeplusv2.bed
test: /Data/Exp1/enrichment
=======================1=======================
>>> STEP 1: reducing files

READS FILE:
/Data/Exp1/s_3_QC_remdup.sam was reduced to /Data/Exp1/1306423511007/NGSrich_s_3_QC_remdup_KDavid.26819.txt
Reduced file /Data/Exp1/1306423511007/NGSrich_s_3_QC_remdup_KDavid.26819.txt sorted

GENOME ANNOTATION FILE:
/Data/Exp1/1306423511007/refGene.genome reduced to /Data/Exp1/1306423511007/NGSrich_genome_KDavid.26819.txt
Exception in thread "main" java.lang.ArrayIndexOutOfBoundsException: Array index out of range: 1
at java.util.Vector.get(Vector.java:721)
at adapter.Adapter.field(Adapter.java:90)
at adapter.TargetAdapter.start(TargetAdapter.java:168)
at adapter.TargetAdapter.adapt(TargetAdapter.java:56)
at Enrichment.reduceFiles(Enrichment.java:185)
at NGSrich.main(NGSrich.java:91)

This is a head result of my .bed file

head /Data/Exp1/exomeplusv2.bed
track:exome
chr1 30275 30431
chr1 69069 70029
chr1 228233 228354
chr1 228471 228711
chr1 367647 368608
chr1 470971 471330
chr1 621084 622045
chr1 741165 741285
chr1 745438 745558

Any ideas?

Thanks,

Dave

[NGSfan]

Hi! I got it to work, the output looks correct! It's strange though I can see Step 3 and Step 5 as unsuccessful, but the output looks finished (includes list of poor and high covered genes).

I really like the summary.



java NGSrich -r /net/ngs/NGS.analysis/data/091204_ILLUMINA-075005_0000_42GHRAAXX/s_1.42GHRAAXX_LIB001_MIAPACA2_24877_FID000.J00001.alnRecal.sam -a /net/ngs/NGS.analysis/bin/annovar/humandb/hg18_refGene.txt -t /net/ngs/NGS.analysis/reference/500_Target_Regions.bed -T /dev/shm/
test: /net/ngs/NGS.analysis/data/091204_ILLUMINA-075005_0000_42GHRAAXX/enrichment
=======================1=======================
>>> STEP 1: reducing files
READS FILE:
/net/ngs/NGS.analysis/data/110415_SN378_0070_B81MCAABXX/s_1.B81MCAABXX_LIB160_HT_26828_FID047_J00229.bfast.sam was reduced to /dev/shm/1305908202090/NGSrich_s_1.B81MCAABXX_LIB160_HT_26828_FID047_J00229.bfast_vieasncl6.20049.txt
Reduced file /dev/shm/1305908202090/NGSrich_s_1.B81MCAABXX_LIB160_HT_26828_FID047_J00229.bfast_vieasncl6.20049.txt sorted

GENOME ANNOTATION FILE:
/dev/shm/1305908202090/hg18_refGene.genome reduced to /dev/shm/1305908202090/NGSrich_genome_vieasncl6.20049.txt

TARGET REGIONS FILE:
/dev/shm/1305908202090/1000plus_Target_Regions.target reduced to /dev/shm/1305908202090/NGSrich_target_vieasncl6.20049.txt
Reduced file /dev/shm/1305908202090/NGSrich_target_vieasncl6.20049.txt sorted

STEP 1 successfully completed

=====================2=========================
>>> STEP 2: computing target coverage data

Starting computing target coverage files.
Mean target coverage data computed (/net/ngs/NGS.analysis/data/110415_SN378_0070_B81MCAABXX/enrichment/s_1.B81MCAABXX_LIB160_HT_26828_FID047_J00229.bfast_enrichment.bed).
Detailed base coverage computed (/dev/shm/1305908202090/coverage_vieasncl6.20049.txt).
Coverage summary computed (/net/ngs/NGS.analysis/data/110415_SN378_0070_B81MCAABXX/enrichment/s_1.B81MCAABXX_LIB160_HT_26828_FID047_J00229.bfast_enrichment.xml).

STEP 2 successfully completed

=====================3=========================
>>> STEP 3: evaluating enrichment files

Detecting evaluation program
"data" and "plots" subdirectories created and xml and bed file moved to the data subdirectory!
Run evaluation program on the following arguments Writing HTML output ... ready.Finished.
HTML FILE /net/ngs/NGS.analysis/data/110415_SN378_0070_B81MCAABXX/enrichment/s_1.B81MCAABXX_LIB160_HT_26828_FID047_J00229.bfast_enrichment.html not found378_0070_B81MCAABXX/enrichment/110415_enrichment.html
Creating coverage barplot ... ready.Searching for poorly (<2x) and highly (>200x) covered genes ...AABXX_LIB160_HT_26828_FID047_J00229.bfast_enrichment.bed
STEP 3 unsuccessfulbarplots ... ready.Creating coverage barplot ...CAABXX/enrichment
Creating coverage pieplot ... ready.Preparing coverage barplots ...efGene.txt
=====================4=========================eplot ...
>>> STEP 4: computing targets wiggle datale ...
R Ausgabe: Reading XML file ...
Start computing target-based wiggle data
Details File Name: /dev/shm/1305908202090/coverage_vieasncl6.20049.txt
Output Dir: /net/ngs/NGS.analysis/data/110415_SN378_0070_B81MCAABXX/enrichment/data
End of computing target-based wiggle data

STEP 4 successfully completed.

=====================5=========================
>>> STEP 5: computing overall wiggle data

Start computing overall wiggle data
Align File Name: /dev/shm/1305908202090/NGSrich_s_1.B81MCAABXX_LIB160_HT_26828_FID047_J00229.bfast_vieasncl6.20049.txt
Output Dir: /net/ngs/NGS.analysis/data/110415_SN378_0070_B81MCAABXX/enrichment/data
/net/ngs/NGS.analysis/data/110415_SN378_0070_B81MCAABXX/enrichment/s_1.B81MCAABXX_LIB160_HT_26828_FID047_J00229.bfast_enrichment.wignot found

STEP 5 unsuccessful

===============================================

[1]+ Done java NGSrich -r /net/ngs/NGS.analysis/data/110415_SN378_0070_B81MCAABXX/s_1.B81MCAABXX_LIB160_HT_26828_FID047_J00229.bfast.sam -a /net/ngs/NGS.analysis/bin/annovar/humandb/hg18_refGene.txt -t /net/ngs/NGS.analysis/reference/1000plus_Target_Regions.bed -T /dev/shm/

[husamia]

It would be nice to include example of report to see what types of metrics it can calculate. I am curious about this.

[pfrommolt]

If you have downloaded and unzipped the annotation from

http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/refGene.txt.gz

(example for hg19), you can just specify the local path to this file instead of 'hg19'.

[NGSfan]

Hi,

Could you add a feature to allow the user to point to an annotation file instead of download it everytime?

[pfrommolt]

Version 0.4.2 uploaded to SourceForge!

Recent changes:
-> SAM header sections are skipped
-> unassembled contigs with less than 3 genes are ignored
-> Bug in the computation of coverage statistics was removed

[pfrommolt]

Yes, we have already prepared a version which can handle the header section adequately. This is coming very soon.

Did your run create a BED and XML file in the 'data' directory? If so, could you email these to my address given in the README file?

Does the SureSelect target file have more than one BED track? You should provide a BED file with only one track.

Regards,
Peter

[bpetersen]

I tried it again after removing the header of my samfile and the previous error is gone, but now I get the following:

=======================1=======================
>>> STEP 1: reducing files

READS FILE:
/home/bpetersen/exome_9_A0019.sam was reduced to /home/bpetersen/temp/1305783668487/NGSrich_exome_9_A0019_cl008.27100.txt
Reduced file /home/bpetersen/temp/1305783668487/NGSrich_exome_9_A0019_cl008.27100.txt sorted

GENOME ANNOTATION FILE:
/home/bpetersen/temp/1305783668487/refGene.genome reduced to /home/bpetersen/temp/1305783668487/NGSrich_genome_cl008.27100.txt

TARGET REGIONS FILE:
/home/bpetersen/temp/1305783668487/TruSeq_exome_targeted_regions.converted.hg18.target reduced to /home/bpetersen/temp/1305783668487/NGSrich_target_cl008.27100.txt
Reduced file /home/bpetersen/temp/1305783668487/NGSrich_target_cl008.27100.txt sorted

STEP 1 successfully completed

=====================2=========================
>>> STEP 2: computing target coverage data

Starting computing target coverage files.
Mean target coverage data computed (/home/bpetersen/NGSricCreating coverage barplot for chr21 ... ready.Creating coverage barplot for chr21_random ...
HTML FILE /home/bpetersen/NGSrich_test/exome_9_A0019_enrichment.html not founddy.Creating coverage barplot for chr21 ...
Coverage summary computed (/hCreating coverage barplot for chr2 ... ready.Creating coverage barplot for chr20 ...
STEP 3 unsuccessfulting coverage barplot for chr19 ... ready.Creating coverage barplot for chr2 ...
Creating coverage barplot for chr18 ... ready.Creating coverage barplot for chr19 ... Creating coverage barplot for chr17_random ... ready.Creating coverage barplot for chr18 .=====================4========================= Creating coverage barplot for chr17 ... ready.Creating coverage barplot for chr17_random ...
>>> STEP 4: computing targets wiggle data====== Creating coverage barplot for chr16 ... ready.Creating coverage barplot for chr17 ...
>>> STEP 3: evaluating enrichment files Creating coverage barplot for chr15 ... ready.Creating coverage barplot for chr16 ...
Start computing target-based wiggle data Creating coverage barplot for chr14 ... ready.Creating coverage barplot for chr15 ...
Details File Name: /home/bpetersen/temp/1305783668487/coverage_cl008.27100.txtlot for chr13 ... ready.Creating coverage barplot for chr14 ...
Output Dir: /home/bpetersen/NGSrich_test/data xml Creating coverage barplot for chr12 ... ready.Creating coverage barplot for chr13 ...
End of computing target-based wiggle datang coverage barplot for chr11 ... ready.Creating coverage barplot for chr12 ...
XML summary file: /hCreating coverage barplot for chr10 ... ready.Creating coverage barplot for chr11 ...
STEP 4 successfully completed.t for chr1 ... ready.Creating coverage barplot for chr10 ...
Preparing coverage barplots ... ready.Creating coverage barplot for chr1 ...
=====================5=========================overage barplots ...
>>> STEP 5: computing overall wiggle dataage pieplot ...
Reading XML file ... ready.Reading BED file ...
Start computing overall wiggle data
Align File Name: /home/bpetersen/temp/1305783668487/NGSrich_exome_9_A0019_cl008.27100.txt
Output Dir: /home/bpetersen/NGSrich_test/data
/home/bpetersen/NGSrich_test/exome_9_A0019_enrichment.wignot found

STEP 5 unsuccessful

===============================================

The plots were successfully generated but not the html file.
Any idea why this might be?
I think it would be great if you could get NGSrich to work with samfiles with header or even better with bamfiles, is this planned anytime soon?

[NGSfan]

The -a and -g flags are equivalent, so you can choose any one of these. The annotation comes from the UCSC track but the download usually finishes within seconds, so you do not need to worry about this.

It is a shame that I am behind a firewall - would it be possible to have the UCSC track file stored locally and accessed by NGSrich instead of downloaded?

[pfrommolt]

The -a and -g flags are equivalent, so you can choose any one of these. The annotation comes from the UCSC track but the download usually finishes within seconds, so you do not need to worry about this.

[NGSfan]

what is the difference between -a and -g options for the annotation?

And where does the annotation come from, the UCSC track?

I ask because I have UCSC track for hg18 already downloaded.

Thanks for sharing your program. I am looking forward to trying it out.

[pfrommolt]

Do you have a header section in your SAM file? Could you please try whether it works after removal of those lines?

Best,
Peter